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1999 220 second gear whines under load and all gears have a slight whine. Pulled apart and found a bad but still working clutch bearing. I'm not sure this would cause the whine under load as in pulling not like the clutch lever being pulled in. Any thoughts?

Replace it and found out! :) Gears will require a case split.

It kind of sounds like the output shaft bearing might going out. I believe that second gear is right next to it. It could also be pitted and or worn 2nd gears.

Ron